def test_collect_types_subset(self):
conv = PDB2LMP("test/data/ala-aa.gro")
conv.collect_types(allow_atom_subset=True)
self.assertListEqual(conv.moltypes, ["0NA"])
self.assertListEqual(conv.atomtypes, ["MEOH", "ETOH", "OXY", "WAT"])
self.assertEqual(conv.natoms.total, 6)
self.assertEqual(conv.natoms.types, 4)
def test_collect_types_no_add_water(self):
conv = PDB2LMP("test/data/glc.pdb")
conv.collect_types(add_water=False)
self.assertListEqual(conv.moltypes, ["0GA"])
self.assertListEqual(conv.atomtypes, ["MEOH", "ETOH", "OXY"])
self.assertEqual(conv.natoms.total, 6)
self.assertEqual(conv.natoms.types, 3)
def test_collect_types_conditional_bond(self):
moldb = MolDatabase("test/data/mol-polyethene.json")
conv = PDB2LMP("test/data/polyethene.gro", moldb=moldb)
conv.collect_types(add_water=False)
self.assertListEqual(conv.moltypes, ["ETH", "ETE"])
self.assertListEqual(conv.atomtypes, ["TAIL"])
self.assertListEqual(conv.lentypes, ["test", "tail-tail"])
self.assertEqual(conv.natoms.total, 10)
self.assertEqual(conv.nlengths.total, 6)
conv.populate_pdb_data()
conv.write_forcefield("polyethene.ff")
conv.write_data("polyethene.data")
def test_collect_types_multiple_residues(self):
conv = PDB2LMP("test/data/glc_crystal.gro")
conv.collect_types()
self.assertListEqual(conv.moltypes, ["0GB"])
self.assertListEqual(conv.atomtypes, ["MEOH", "ETOH", "OXY", "WAT"])
self.assertListEqual(conv.lentypes, ["sugar-ring"])
self.assertListEqual(conv.angtypes, ["sugar-ring"])
self.assertEqual(conv.natoms.total, 576)
self.assertEqual(conv.natoms.types, 4)
self.assertEqual(conv.nlengths.total, 576)
self.assertEqual(conv.nlengths.types, 1)
self.assertEqual(conv.nangles.total, 576)
self.assertEqual(conv.nangles.types, 1)
self.assertEqual(conv.ndihedrals.total, 576)
self.assertEqual(conv.ndihedrals.types, 2)
self.assertEqual(conv.nimpropers.total, 480)
def test_collect_types_full(self):
conv = PDB2LMP("test/data/glc.pdb")
conv.collect_types()
self.assertListEqual(conv.moltypes, ["0GA"])
self.assertListEqual(conv.atomtypes, ["MEOH", "ETOH", "OXY", "WAT"])
self.assertListEqual(conv.lentypes, ["sugar-ring"])
self.assertListEqual(conv.angtypes, ["sugar-ring"])
self.assertEqual(conv.natoms.total, 6)
self.assertEqual(conv.natoms.types, 4)
self.assertEqual(conv.nlengths.total, 6)
self.assertEqual(conv.nlengths.types, 1)
self.assertEqual(conv.nangles.total, 6)
self.assertEqual(conv.nangles.types, 1)
self.assertEqual(conv.ndihedrals.total, 6)
self.assertEqual(conv.ndihedrals.types, 2)
self.assertEqual(conv.nimpropers.total, 5)
self.assertEqual(conv.nimpropers.types, 2)
def test_write_forcefield_mixed(self):
conv = PDB2LMP("test/data/mixed.pdb")
conv.collect_types()
conv.populate_pdb_data()
conv.write_forcefield("mixed.ff")
def test_write_data(self):
conv = PDB2LMP("test/data/water.pdb")
conv.collect_types()
conv.populate_pdb_data()
conv.write_data("water.data")
def test_populate_pdb_data(self):
conv = PDB2LMP("test/data/water.pdb")
conv.collect_types()
conv.populate_pdb_data()
self.assertEqual(conv.coords.atoms[0].type, "WAT")
def test_read_data(self):
conv = PDB2LMP("test/data/water.pdb")
def test_gro(self):
conv = PDB2LMP("test/data/water.gro")
conv.collect_types()
conv.populate_pdb_data()
conv.write_data("from_gro.data")
conv.write_forcefield("from_gro.ff")
def test_glc(self):
conv = PDB2LMP("test/data/glc.pdb")
conv.collect_types()
conv.populate_pdb_data()
conv.write_data("glc.data")
conv.write_forcefield("glc.ff")
def test_collect_types(self):
conv = PDB2LMP("test/data/water.pdb")
conv.collect_types()
self.assertListEqual(conv.moltypes, ["WAT"])
self.assertListEqual(conv.atomtypes, ["WAT"])